Evolutionary dynamics of viral attenuation

The genetic trajectory leading to viral attenuation was studied in a canine parvovirus (CPV) strain grown on dog kidney cells for 115 transfers. Consensus sequences of viral populations at passages 0, 3, 30, 50, 80, and 115 were obtained from PCR products covering 86% of the genome; clones from each of the 80th and 115th passages were also sequenced, covering 69% of the genome. Sixteen changes were fixed in the 115th-passage virus sample. Levels of polymorphism were strikingly different over time, in part because of a plaque-cloning step at passage 112 that reduced variation: passage 80 had 19 variants common among the clones, but passage 115 had only a single common variant. Several mutations increased in the culture at the same time, with most reaching fixation only after the 80th passage. The pattern of evolution was consistent with recombination and not with separate selective sweeps of individual mutations. Thirteen of the changes observed were identical to or at the same positions as changes observed in other isolates of CPV or feline panleukopenia virus.     

Immune-mediated attenuation of HIV-1

Immune escape mutations selected by human leukocyte antigen class I-restricted CD8(+) cytotoxic T lymphocytes (CTLs) can result in biologically and clinically relevant costs to HIV-1 replicative fitness. This phenomenon may be exploited to design an HIV-1 vaccine capable of stimulating effective CTL responses against highly conserved, mutationally constrained viral regions, where immune escape could occur only at substantial functional costs. Such a vaccine might 'channel' HIV-1 evolution towards a less-fit state, thus lowering viral load set points, attenuating the infection course and potentially reducing the risk of transmission. A major barrier to this approach, however, is the accumulation of immune escape variants at the population level, possibly leading to the loss of immunogenic CTL epitopes and diminished vaccine-induced cellular immune responses as the epidemic progresses. Here, we review the evidence supporting CTL-driven replicative defects in HIV-1 and consider the implications of this work for CTL-based vaccines designed to attenuate the infection course.     

Pharmacological attenuation of Paramecium fluid-phase endocytosis

Spectrophotometric quantification of fluid phase endocytosis in the presence of different pharmacological compounds was performed in the model unicellular eukaryote Paramecium. The kinetics of Lucifer Yellow Carbohydrazide (LY) uptake in cells exposed to forskolin and isoproterenol--known to stimulate phagocytosis in this cell--was analyzed. Reduction in both the rate of endocytosis and total accumulation of fluid phase marker was observed following the treatment. Forskolin diminished total LY accumulation by 11% and 21% after 5 min and 25 min of incubation, respectively, whereas the rate of uptake was lowered by 21% in comparison to control cells. The inhibitory effect ofisoproterenol was less pronounced than that of forskolin. The total accumulation of LY was decreased by 11% in 5 min as compared to the untreated cells and this effect was persistent upon further exposition to this reagent up to 25 min. To better understand these observations, the effect of inhibitors of PKA and cAMP phosphodiesterase on fluid phase uptake was tested. 3-isobutyl-1-methyl xanthine (IBMX) caused 12% decrease in LY accumulation after 5 min of incubation. In combination with isoproterenol or forskolin, IBMX enhanced their inhibitory effect on fluid endocytosis, which was lowered by 25% and 29%, respectively. The strongest inhibitory effect on fluid endocytosis was exerted by the 10 microM PKA inhibitor, which diminished endocytosis by 35% in 5 min. These results suggest that Paramecium fluid phase uptake may be regulated through activation of PKA, although the precise mechanism of this process has not yet been elucidated.     

Oncogene addiction: role of signal attenuation

Tumors can become dependent upon signaling by oncogenes. In a recent issue of Cancer Cell, Sharma et al. (2006b) reported that "oncogene addiction" may be mediated by differential rates of signal attenuation of proapoptotic and prosurvival pathways.     

Relationship between attenuation coefficients and dose-spread kernels

Dose-spread kernels can be used to calculate the dose distribution in a photon beam by convolving the kernel with the primary fluence distribution. The theoretical relationships between various types and components of dose-spread kernels relative to photon attenuation coefficients are explored. These relations can be valuable as checks on the conservation of energy by dose-spread kernels calculated by analytic or Monte Carlo methods.     

Pentoxifylline attenuation of experimental hepatopulmonary syndrome.

Hepatopulmonary syndrome (HPS) following rat common bile duct ligation results from pulmonary molecular changes that may be influenced by circulating TNF-alpha and increased vascular shear stress, through activation of NF-kappaB or Akt. Increased pulmonary microvascular endothelin B (ET(B)) receptor and endothelial nitric oxide synthase (eNOS) levels contribute to nitric oxide production and the development of experimental HPS. Pentoxifylline (PTX), a phosphodiesterase and nonspecific TNF-alpha inhibitor, ameliorates experimental HPS when begun before hepatic injury. However, how PTX influences the molecular events associated with initiation of experimental HPS after liver injury is established is unknown. We assessed the effects of PTX on the molecular and physiological features of HPS in vivo and on shear stress or TNF-alpha-mediated events in rat pulmonary microvascular endothelial cells in vitro. PTX significantly improved HPS without altering portal or systemic hemodynamics and downregulated pulmonary ET(B) receptor levels and eNOS expression and activation. These changes were associated with a reduction in circulating TNF levels and NF-kappaB activation and complete inhibition of Akt activation. In rat pulmonary microvascular endothelial cells, PTX inhibited shear stress-induced ET(B) receptor and eNOS expression and eNOS activation. These effects were also associated with inhibition of Akt activation and were reproduced by wortmanin. In contrast, TNF-alpha had no effects on endothelial ET(B) and eNOS alterations in vitro. PTX has direct effects in the pulmonary microvasculature, likely mediated through Akt inhibition, that ameliorate experimental HPS.     

Fluoxetine-induced attenuation of amphetamine self-administration in rats

Daily injections of fluoxetine (5.0 mg/kg i.p.) to rats trained to self-administer intravenous d-amphetamine produced marked decreases in drug intake on three successive days of treatment. After fluoxetine injections were stopped, the number of daily amphetamine self-injections was still significantly reduced for an additional 2 days. When trained amphetamine self-administration animals were placed in an apparatus which delivered i.v. saline with each lever press, increased self-injection is observed. Acute fluoxetine injection did not alter this response. However, if fluoxetine is given prior to amphetamine exposure for 1 day and animals are then tested for the saline response, lever pressing activity is significantly reduced. These data might suggest that 5-hydroxytryptaminergic neurons mediate some aversive or negative reinforcing property of amphetamine. If true, this finding could be exploited clinically in cases of human psychomotor stimulant addiction.     

Soft tissue attenuation of acoustic emission pulses

The soft tissue attenuation of acoustic emission signals was measured by transmitting pulses through volunteers and measuring the decay of the waveform characteristics of the pulse as a function of the thickness of the interposed tissue. Waveform characteristics of the received signal (signal duration, number of counts, peak amplitude, energy, and rise time) demonstrated an exponential decrease with increasing tissue thickness. The decrease appeared insensitive to the frequency of the pulse within the range of 50 to 600 KHz.     

高发酵度酵母的筛选及鉴定

主要研究了Saccharomyces cerevisiae wx、Saccharomyces cerevisiae qp、Saccharomycescerevisiae nq、Saccharomyces cerevisiae cx、Saccharomyces cerevisiae hs和Saccharomyces cerevisiae3322(以下简称S.C.wx、S.C.qp、S.C.nq、S.C.cx、S.C.hs和S.C.3322)6株酵母菌的形态、同化氮源、发酵力、α-葡萄糖苷酶活力等生理特性,通过实验比较发现S.C.nq和S.C.cx两株菌种在利用糖的种类、同化氮源、真正发酵度及α-葡萄糖苷酶活力等方面较高,因此对这两株菌种进行了还原双乙酰、糖代谢两方面性质的比较,结果表明:两株菌种在还原双乙酰、糖代谢两方面效果显著,筛选出两株优良的高发酵度啤酒酵母菌种。     

Elucidating the microbial component of natural attenuation

Microbial reactions are a key determinant in natural attenuation. However, providing unequivocal evidence of the extent of their involvement is challenging. Several approaches are being developed to meet this challenge, including the use of contaminant-specific transformation products, carbon- or hydrogen-based stable isotopic analysis and reactive transport modeling. These approaches emphasize the ongoing need to integrate strategically between temporally and spatially variant geochemical conditions, the ecological characteristics of the resident microbial communities and their resultant pollutant-transformation capabilities.     

Narrow terahertz attenuation signatures in Bacillus thuringiensis

Terahertz absorption signatures from culture‐cultivated Bacillus thuringiensis were measured with a THz photomixing spectrometer operating from 400 to 1200 GHz. We observe two distinct signatures centered at ～955 and 1015 GHz, and attribute them to the optically coupled particle vibrational resonance (surface phonon‐polariton) of Bacillus spores. This demonstrates the potential of the THz attenuation signatures as “fingerprints” for label‐free biomolecular detection. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

A theoretical study of the attenuation control mechanism

The attenuator control mechanism, used in a number of amino acid biosynthetic operons, is considered from a theoretical point of view. The physics of RNA hairpin-loop formation is discussed, and rules for predicting which codons in the leader peptide that will affect operon expression are suggested. Manabe's (1981) stochastic model for the attenuator mechanism is used to analyse a number of known attenuators, showing a need for a “polymerase pause-site” in most of the attenuators, and providing some quantitative arguments in favour of the use of unusual codons in the control region.